Dr Patricia Rojas Sanchez PhD

Institute of Applied Health Research
Research Fellow

Contact details

Address
Institute of Translational Medicine (ITM)
Heritage Building
University of Birmingham
Edgbaston
Birmingham
B15 2TT
UK

Patricia is an exceptionally versatile PhD, with specialties in microbiology, HIV and Bioinformatics research. She is happy working diligently either as an individual or as part of a team; addressing and calmly resolving problems even under pressure. Her creative outlook drives continuous improvement through seeking innovative solutions, with a natural ability to refine processes and bring the best out of her team. Her proven ability to deliver work successfully is a result of a full commitment which builds trust and respect leading to project success. She brings enthusiasm and a positive attitude to any team environment, fostering a collaborative and transparent work ethic.

Qualifications

  • PhD in Molecular Biology (Cum Laude distinction), Universidad Autónoma de Madrid, January 2017
  • MSc Bioinformatics and Computational Biology, Escuela Nacional de Sanidad, Madrid, October 2014 - May 2015
  • MSc Microbiology and Parasitology, Universidad Complutense de Madrid, Madrid, Oct. 2011 - July 2012
  • BSc (Hons) Biology, Universidad Complutense de Madrid, Madrid, Oct. 2005 - Feb. 2011

Biography

During the last two years, Patricia has been working as a Bioinformatician at the University of Birmingham (cancer and genomic science) in Saponaro group. During this period, she analysed “omics data” and established pipelines for ChIP-seq, RNA-seq and Repli-seq in different samples, enhancing her confidence in carrying out genome wide analysis. As the only bioinformatician in the team, she gained wide experience solving problems, using her own initiative and working closely with her colleagues.

In January 2017, Patricia finished her PhD in HIV-1 Molecular Epidemiology and the implications of AIDS in perinatally infected children and adolescents  As part of her PhD project, she has analysed clinical, immunological and virological follow-up in perinatally HIV-1nfected children and adolescents from the Madrid Cohort.

Several projects have been accepted for publication by international scientific journals:

Patricia gained wide experience using human data, big databases and analysing the results obtained to improve clinical management of HIV-1 nfected children carrying triple resistance in Spain. A key inspiration has been the realisation that this work can contribute to develop future therapeutic options through different drug combinations.

As part of her PhD, Patricia has worked in Stanford University with Dr. Robert Shafer, analysing a high number of HIV-1 sequences and their factors to modulate the evolution of HIV infected patients.  During this period, she learnt an extensive amount of bioinformatics programming skills. 

Patricia is keen to continue her career in bioinformatics focussing predominantly on the analysis and management of clinical and epidemiological data.

Research

  • April 2019 -Present.  University of Birmingham, Institute of Applied Health Research & ITM. 

To describe how microorganisms and immunological events in pregnancy and early life, interact with genetic and epigenetic factors, sociodemographic and clinical factors to influence human health across the life cycle.

  • Nov. 2016 – March. 2019. University of Birmingham, Institute of Cancer and Genomic Science

Responsible for all the bioinformatic analysis ( a combination of ChIP-Seq, RNA-Seq and Repli-seq) in order to characterise RNA Pol II transcription progression in transcription defective contexts, investigating also how these defects impact on genome stability. Variant calling analysis in uterine cancre samples and analysis of gene expression levels (RNA-seq and differential exon usage) in chronic lymphocytic leukaemia samples.

  • 2015, Stanford University. School of Medicine Infectious: Diseases and Geographic Medicine. Stanford, CA

Analysis of protease and retrotranscriptase sequence datasets from approximately 100,000 HIV infected individuals and integrase sequences from about 10,000 HIV-infected individuals in order to characterize the observed variation at each amino acid position in each gene. Development of a web interface (http://hivdb.stanford.edu/cgi-bin/Probe.cgi) to provide the information of the variation in a selected amino acid position and the flanking sequences of its position. Software development (using Perl language) to determine the genetic distances between sequences and network analysis.

  • 2012 – 2015, Hospital Ramón y Cajal. HIV-1 Molecular Epidemiology Laboratory. Madrid, Spain

Analysis of the molecular evolution in HIV-1 infected children. Study of the effect of clinical factors in the evolution of HIV-1 subtype B in paediatrics patients. Analysis of clinical, immunological and virological follow-up in perinatally HIV-1-infected children and adolescents from the Madrid Cohort with triple-class antiretroviral drug resistant viruses. Study of gestational parameters in HIV-infected mothers, and in HIV perinatally infected children and adolescents from the Madrid cohort and determining the rate of HIV vertical transmission in such cohort.

  • 2012 – October 2017, Madrid Paediatric Cohort of HIV-1 infected Children and adolescents. Madrid, Spain

Study and analysis of epidemiological and clinical data of the patients involved in the cohort of pregnant women with HIV infection and their children in Madrid. Evaluation of the efficacy and safety of antiretroviral therapy in the mother and the child as prevention vertical transmission of HIV-1 and hepatitis C virus.

  • 2011 – 2012, Universidad Complutense de Madrid School of Medicine: Department of Molecular Biology. Madrid, Spain 

Study of the oxidative stress processes in obese rat and its gene expression variation. Wide experience experience based on PCR and RT-PCR.

  • 2010 – 2011, Biological Investigation Center (CIB-CSIC). Department of Molecular Microbiology and Infection, Madrid, Spain

Study of the expression, cloning and modification of Gram positive bacteria. Development of plasmids allowing the expression of the fluorescent protein mCherry.

Publications

Bowry A, Piberger AL, Rojas P, Saponaro M, Petermann E. BET Inhibition Induces HEXIM1- and RAD51-Dependent Conflicts between Transcription and Replication. Cell Rep. 2018. 20;25(8):2061-2069.e4

Rojas Sánchez P, Dominguez S, Jiménez de Ory S, Prieto L, Rojo P, Mellado MJ, Navarro M, Delgado R, Ramos JT and Holguín A. Trends in drug resistance prevalence, HIV-1 variants and clinical status in HIV-1-infected paediatric population in Madrid: 1993-2015 Analysis. PediatrInfect Dis J, 2018 Mar;37(3):e48-e57

Domínguez-Rodríguez S, Rojas Sánchez P, Fernández Mcphee C, Pagán I, Navarro M, Ramos JT and Holguin A. Effect of HIV/HCV Co-Infection on the Protease Evolution of HIV-1B: A Pilot Study in a Pediatric Population.Sci Rep. 2018; 8:2347.

Rojas Sánchez P, Cobos A, Navarro M, Ramos JT, Pagan I and Holguín A. Impact of Clinical Parameters in the Intrahost Evolution of HIV-1 Subtype B in Pediatric Patients: A Machine Learning Approach. Genome Biol Evol. 2017. 1;9(10):2715-2726.

Rojas Sánchez P, Prieto L, Jiménez de Ory S, Fernández Cooke, E, Navarro M, Ramos JT and Holguín A. Impact of exposure to lopinavir-ritonavir in HIV-1 infected children and adolescents in Madrid, Spain during 2000-2014. PLoS One. 2017. 28;12(3):e0173168.

Prieto L, Fernández McPhee C, Rojas Sanchez P, Mazariegos D, Muñoz E, Holguín A, Mellado MJ, Navarro ML, González Tomé MI and Ramos JT; on behalf of the Madrid Cohort of HIV-infected Mother-Infant Pairs. Pregnancy outcomes in perinatally HIV-infected young women in Madrid, Spain: 2000-2015 analysis. PLoS One. 2017. 2(8):e0183558.

Pagán I, Rojas Sánchez P, Ramos JT, Holguín A. Clinical determinants of HIV-1B between-host evolution and their association with drug resistance in pediatric patients. Plos One. 2016. 11(12):e0167383.

Clutter D, Rojas Sánchez P, Rhee SY and Shafer R. Genetic Variability of HIV1 for Drug Resistance Assay Development. Viruses. 2016. 8:48.

Fernandez-Cooke E, Rojas Sánchez P, Jimenez de Ory S, Bellón J.M, Holguín A, Mellado MJ, Gonzalez Tomé MI, Ramos JT. Description and consequences of prescribing off-label antiretrovirals in the Madrid Cohort of HIV-infected children over a quarter of a century (1988-2012). Antiviral Therapy. 2016. 21(1):65-70

Rojas Sánchez P, de Mulder M, Fernandez-Cooke E , Prieto L, Rojo P, Jiménez de Ory S, Navarro ML, Ramos JT, Holguín A. Clinical and virological follow-up in perinatally HIV-1infected children and adolescents in Madrid with triple-class antiretroviral drug resistant viruses. Clin Microbiol Infect. 2015. 21(6):605.e1-9.  Page 4 of 7Patricia Rojas Sánchez 11/2018

Rojas Sánchez P and Holguín A. Drug resistance in HIV-1 infected paediatric population worldwide: a systematic review. J Antimicrob Chemother. 2014. 69(8):2032-42.

Prieto LM, González-Tomé MI, Muñoz et al. Madrid Cohort of HIV-Infected Mother-Infant Pairs. Birth defects in a cohort of infants born to HIV-infected women in Spain, 2000-2009. BMC Infect Dis. 2014. 24;14:700.